Search Results (1,803)

To overcome the seasonal constraints of explant availability and facilitate genetic improvement in Catalpa ovata, this study established a dual-pathway in vitro regeneration system (encompassing adventitious shoot organogenesis and somatic embryogenesis) using mature zygotic embryos. We systematically evaluated the synergistic effects of maternal genotypes, plant growth regulators (PGRs), basal media, and the histone deacetylase inhibitor Trichostatin A (TSA). Genotype screening revealed significant divergence in regenerative potential, with the half-sib family 32F17 exhibiting superior responsiveness (84.7% callus induction). A high cytokinin-to-auxin ratio (ZA3 medium) optimally drove direct shoot organogenesis. For adventitious shoot proliferation, the addition of TDZ significantly improved the multiplication coefficient (up to 2.99 on ZB4 medium), although a physiological trade-off with shoot elongation was observed. In parallel, the application of 10 µM TSA significantly enhanced somatic embryogenesis from embryogenic calli, effectively alleviating the inhibitory constraints of exogenous PGRs. For rhizogenesis, the DKW basal medium proved superior to half-strength MS, with the ZE3 treatment (0.1 mg·L⁻¹ NAA + 0.1 mg·L⁻¹ IBA) yielding the highest rooting frequency (69.6%) and robust root architecture. Notably, while somatic embryo conversion remained recalcitrant, plantlets derived exclusively from the adventitious shoot organogenesis pathway were successfully acclimatized ex vitro. These transplanted plantlets exhibited consistently high survival rates (83.1–84.4%) across all tested genotypes, effectively overcoming the initial genotype-dependent recalcitrance. Collectively, this optimized protocol provides a reliable technical platform for the large-scale clonal propagation and biotechnological breeding of C. ovata. Full article

Background: Hepatitis E virus (HEV) is an increasingly recognized cause of acute viral hepatitis in Thailand as the burden of hepatitis A, B, and C has declined. HEV is a positive-sense RNA virus in the family Hepeviridae with three major open reading frames encoding replication proteins (ORF1), the capsid protein (ORF2), and an accessory protein involved in viral egress (ORF3). Unlike highly endemic regions where genotypes 1 and 2 are linked to waterborne outbreaks, infections in Thailand are reported mainly as sporadic cases associated with zoonotic transmission, most commonly genotype 3. Objectives: This review summarizes the epidemiology, transmission routes, and public health implications of HEV infection in Thailand. Methods: Peer-reviewed studies on HEV seroprevalence, molecular epidemiology, and transmission in Thailand were identified through PubMed using combinations of the keywords “HEV” and “Thailand”. Two investigators independently screened titles, abstracts, and full texts. Eligible studies were synthesized qualitatively. Results: Earlier studies suggested low population exposure, but more recent evidence indicates substantial cumulative risk. A nationwide survey among blood donors reported anti-HEV IgG seroprevalence of about 30%, with geographic variation and increasing prevalence with age. Detection of HEV RNA in pigs, slaughterhouse environments, and retail pork products, together with links to raw or undercooked pork consumption, supports pigs as the principal reservoir and foodborne exposure as an important route. Transfusion-associated infection has also been documented. Conclusions: In Thailand, HEV infection is linked mainly to zoonotic and foodborne transmission involving genotype 3. Stronger surveillance, food safety measures, and risk-based blood safety policies are needed. Full article

Drought stress poses a significant challenge to food security in sub-Saharan Africa, particularly for smallholder farmers in dryland systems. Bambara groundnut (Vigna subterranea (L.) Verdc.), an underutilised legume with inherent drought tolerance, remains underexplored in terms of its root system traits. This greenhouse study investigated the early root and shoot responses of six Bambara groundnut genotypes under well-watered (100% field capacity) and water-stressed (50% field capacity) conditions using rhizotron-based phenotyping. Significant genotypic differences (p < 0.01) were observed in root traits such as root system depth (RSD: 11.0–19.9 cm), root system width (RSW: 6.96–12.2 cm), and root dry mass (RDM: 0.42–1.27 g). The ARC genotype exhibited a strong drought-avoidance strategy, increasing RSD from 12.2 to 19.9 cm and RDM from 0.42 to 1.16 g under stress. The Tiga Nicuru DIP-C-F7471 genotype showed adaptive plasticity, maintaining deeper roots (11.0–14.5 cm), high convex hull area (CHA), and root–shoot ratio (RSR) values, despite a reduction in RDM, suggesting a resource-conserving strategy. Principal Component Analysis (PCA) captured 93.6% of the total variability among genotypes. Root traits, particularly total root length (TRL), convex hull area (CHA), root system width (RSW), and root dry mass (RDM), were the main contributors to genotype differentiation. Strong positive correlations (r = 0.88–0.97) between root and shoot traits suggest that genotypes with more developed root systems also supported greater shoot growth, highlighting the coordinated response of above- and below-ground traits under drought stress. These findings provide valuable targets for breeding and highlight the value of rhizotron-based screening for root trait selection. Future field validation and full-season studies are recommended to confirm their relevance for improving yield stability in dryland agriculture. Full article

The insulin-like growth factor 1 (IGF-1) gene plays a key role in growth and production traits in livestock. Limited information is available regarding its genetic polymorphisms in Saudi camel breeds. This study aimed to investigate genetic variation in the IGF-1 gene among Saudi camel breeds to provide baseline genetic information for future association studies. A total of 176 camels representing six Saudi breeds were sampled. DNA was extracted and Polymerase chain reaction (PCR) amplification and Sanger sequencing were applied to detect IGF-1 polymorphisms. Genotype and allele frequencies were calculated across breeds, and statistical comparisons were performed based on proportional distributions to account for unequal sample sizes. Two single-nucleotide polymorphisms (SNPs) were identified: c.365G>A in exon 3 and c.435C>T in exon 5. The exon 3 variant resulted in a missense mutation (p. Arg122His) but was detected in heterozygous form in only one camel, and subsequent screening of 109 additional samples confirmed its rarity. The exon 5 variant was synonymous in isoform X1 and located in the 3′ untranslated region of isoform X2. Sequencing of 176 camels revealed that c.435C>T was highly polymorphic across the examined breeds. Significant differences in genotype frequencies were observed within and among breeds (p < 0.001). The CT genotype predominated in Waddah (60%), Shageh (48%), and Sofor (60%), significantly exceeding CC and TT frequencies (p < 0.001). In Majaheem and Saheli, CT (47%) and TT (45%) were nearly equal and both significantly higher than CC (p < 0.001). Shaele exhibited a distinct pattern, with TT being most frequent (57%), significantly higher than CC (7%, p < 0.001) and CT (36%, p < 0.01). These findings indicate directional selection favoring the C allele in the Waddah and Shageh breeds, whereas the T allele is favored in the remaining breeds. This study provides the first baseline characterization of IGF-1 polymorphisms among Saudi camel breeds. Although no phenotypic associations were assessed, the results offer a foundation for future research examining relationships between IGF-1 variants and economically important traits. Full article

Genome-wide association studies (GWASs) are powerful and flexible tools for identifying single nucleotide polymorphisms (SNPs) associated with quantitative traits (yield, stress resistance) in plants. Variable selection and machine learning are two effective approaches in GWAS. However, both face limitations in complex, noisy data analysis in the big-data era. In this study, we integrated variable selection and machine learning under the mixed linear model framework, proposing a novel method, the improved LASSO screening and sparse Bayesian learning algorithm (ILSBL). The ILSBL first corrects the polygenic and environmental noise, then reduces genotypic dimensionality by LASSO-based variable selection, and finally performs parameter estimation using sparse Bayesian learning. Two simulation experiments and association analyses of three flowering-time-related traits in Arabidopsis thaliana were conducted to validate the new algorithm. The results showed that, compared to established methods, the ILSBL exhibited flexibility in simulation studies and maintained robust performance under complex genetic backgrounds, achieving a favorable balance among statistical power, parameter estimation accuracy, runtime efficiency, and false-positive rate. The analysis of the real Arabidopsis datasets further confirmed the advantages of ILSBL for GWASs, with 30 candidate genes adjacent to significant quantitative trait nucleotides (QTNs) associated with flowering-related traits. These results provide valuable insights for a better understanding of the genetic basis underlying flowering-related traits in Arabidopsis. Full article

To establish standardized DNA fingerprinting and molecular identification systems for mandarin citrus, we analyzed 69 mandarin accessions via fluorescent SSR capillary electrophoresis to construct DNA molecular fingerprints and unique molecular identity cards. Eighteen highly polymorphic SSR primer pairs were screened, yielding 239 genotype calls and 147 alleles. The number of amplified alleles per primer pair ranged from 4 to 18, with polymorphic information content (PIC) values varying from 0.411 to 0.650. Ten core primer pairs were further selected, achieving a discrimination rate of 65.2% (45 out of 69 accessions distinguished). Utilizing these fluorescent SSR markers, we established DNA molecular fingerprints and unique molecular identity cards for all 69 accessions. Among them, 45 accessions possessed unique fingerprints, whereas the remaining 24 indistinguishable accessions were clustered into six groups. Each cluster contained both wild (4 accessions total) and cultivated (20 accessions total) resources with high genetic similarity, which merits further investigation. This study provides a practical foundation for the authentication, conservation, and genetic relationship analysis of mandarin germplasm resources and establishes a technical framework for standardizing mandarin variety identification. Full article

Despite the growing knowledge about ovarian cancer, it has not yet been possible to develop an effective screening test for this cancer. Therefore, it seems necessary to identify new risk factors, such as genetic polymorphisms. The aim of this study was to demonstrate whether polymorphisms of the ESR1 gene rs2234693 and rs9340799 may be involved in the development of ovarian cancer. The material for the study was DNA obtained from 100 ovarian cancer patients and 100 control groups. Polymorphisms were determined using the PCR-RFLP technique. The presence of the CC genotype (rs2234693) has been shown to more than double the risk of ovarian cancer (OR 2.21; p = 0.041). In the case of the second polymorphism, rs9340799, the carrier of the GG genotype more than doubles the risk of ovarian cancer (OR 2.62 p = 0.031). Analysis of ESR1 gene haplotypes in relation to the rs2234693 and rs9340799 polymorphisms showed that the occurrence of TCAG and CCGG systems may be associated with a significant increase in the risk of ovarian cancer (OR 1.98, p = 0.043 and OR 2.45, p = 0.041, respectively). In the group of patients with ovarian cancer, a correlation was shown between the polymorphisms rs2234693 and rs9340799 in the tissues of ovarian cancers with the lowest stage compared to more advanced ovarian cancers, which may indicate a relationship between these factors and the stage of the tumor. Women’s age had no effect on the prevalence of individual genotypes or the associated risk of disease. Polymorphisms rs2234693 and rs9340799 of the ESR1 gene may be associated with the occurrence of ovarian cancer. Full article

Tick-borne encephalitis virus (TBEV) is primarily transmitted by Ixodes spp. and poses significant health risks, leading to morbidity and mortality in humans. Two of the five subtypes, Siberian and Far Eastern are known to circulate in Mongolia. In 2021, Ixodes persulcatus ticks were collected from Bulgan aimag (province) using flagging and dragging methods and subsequently screened for TBEV using PCR. Positive samples underwent sequencing using an Oxford Nanopore Technologies-based hybrid capture approach, resulting in two coding-complete TBEV genomes from separate tick pools. Phylogenetic analysis classified both genomes within the Siberian subtype, grouping them with other Mongolian sequences from I. persulcatus collected in 2014, 2020, 2021, and 2023. The study sequences, PX654173 and PX654174, showed high genetic similarity (99.9% and 99.8%, respectively) to the sequence PQ479142, obtained from I. persulcatus ticks in Selenge, Mongolia, in 2021. The estimated time to most recent common ancestor (TMRCA) of the Siberian genotype was approximately 981 CE (95% HPD: 646–1347) with the emergence of a distinct Mongolian clade of TBEV around 1888 CE (95% HPD: 1834–1934). These findings highlight the value of expanded whole-genome sequencing to improve our understanding of TBEV’s genetic diversity and evolutionary history in Central Asia. Full article

Background/Objectives: Non-classical congenital adrenal hyperplasia (NCCAH) due to 21-hydroxylase deficiency represents the mildest form of congenital adrenal hyperplasia and is frequently diagnosed only after the onset of clinical signs in childhood. Newborn screening programs for CAH are primarily designed to detect classical forms and show limited sensitivity for NCCAH. The clinical significance of neonatal 17-hydroxyprogesterone (17-OHP) values below recall thresholds remains incompletely defined. Methods: We retrospectively analyzed clinical, auxological, hormonal, and genetic data from pediatric patients diagnosed with NCCAH between 2018 and 2023 at a tertiary referral center. Neonatal screening 17-OHP concentrations, basal and ACTH-stimulated 17-OHP levels at diagnosis, bone age advancement, pubertal status, and hydrocortisone treatment were evaluated. Correlations between hormonal parameters, age at onset, and treatment dose were assessed. Results: Thirty-five patients (30 females) were included, with a mean age at clinical onset of 7.52 ± 0.36 years for females and 6.25 ± 0.29 years for males. Premature pubarche was the most frequent presenting sign (94.3%), and central precocious puberty was diagnosed in 31.4% of cases. The mean neonatal screening 17-OHP level was 4.53 ± 0.7 ng/mL; only two patients exceeded the screening recall cut-off. At diagnosis, mean basal and ACTH-stimulated 17-OHP levels were 15.1 ± 3.35 and 55.2 ± 11.3 ng/mL, respectively. Age at clinical onset was inversely correlated with both basal and stimulated 17-OHP levels, while hydrocortisone dose correlated positively with biochemical severity. Bone age advancement was observed in all patients. Conclusions: Most children with NCCAH display mildly elevated neonatal 17-OHP values that do not trigger screening recall. Higher biochemical severity is associated with earlier clinical presentation and higher glucocorticoid requirements. Neonatal 17-OHP concentrations, even when below cut-off values, may represent an early indicator of disease severity and warrant further investigation. Full article

Soil salinity remains a major constraint to rice productivity, particularly during early developmental stages when plants are highly sensitive to osmotic and ionic stress. In this study, we evaluated 201 genetically diverse rice genotypes from the 3K Rice Diversity Panel to investigate stage-specific mechanisms of salinity tolerance and develop machine learning-based predictive models for rapid phenotypic screening. Morphological and physiological traits were measured under control and saline conditions at germination and early seedling stages to derive Stress Tolerance Indices (STIs). The average membership function value (AMFV), calculated from multi-trait STI profiles, effectively captured variation in salinity responses and enabled classification of genotypes into five tolerance categories. Genome-wide association analysis using high-density SNP markers identified 36 significant marker–trait associations, including potentially novel SNPs on chromosomes 1 and 12. Several loci co-localized with candidate genes (LTR1, LGF1, OsCPS4, OsNCX7, and OsNHX4), while functional SNPs within genes (OsDRP2C, RLCK168, and OsMed37_2) and non-synonymous variants (qSVII11.1 and qSNaK3.1) further supported their candidacy in salinity tolerance. Mining favourable SNPs of causal genes identified superior multilocus combinations consistent with STI-based phenotypic patterns, with genotype 91-382 emerging as the strongest performer, exhibiting enhanced Na⁺ exclusion, K⁺ retention, and biomass resilience across developmental stages. To address multicollinearity among STI traits, we applied cross-validated LASSO (germination) and Elastic Net (early seedling) models, achieving high predictive accuracy and revealing a developmental shift from biomass-driven tolerance at germination to ion-regulatory processes at the seedling stage. Independent validation showed strong agreement between predicted and observed AMFVs. By integrating physiological indices, GWAS-derived SNP signals, and regularized machine learning approaches, this study provides a robust framework for identifying elite donors and accelerating breeding for salt-tolerant rice. Full article

Carcass growth and development are crucial evaluation indicators influencing the economic efficiency of goats (Capra hircus). This study aimed to screen the nucleotide variation sites (SNPs) of the APOE gene in Guizhou white goats and explore the correlation between APOE gene variations and body size traits, as APOE had been identified as a key candidate gene regulating growth and development in this breed through transcriptome sequencing screening. A total of 324 Guizhou white goats were used in this study for SNP detection, population genetic analysis, real-time fluorescence quantitative PCR (RT-qPCR) and association analysis. The results showed that one nucleotide mutation site (g.353 A > G) was detected in the APOE gene, which yielded two alleles (A and G) and three genotypes (AA, AG and GG). The site exhibited moderate polymorphism and conformed to Hardy–Weinberg equilibrium. The mRNA expression level of APOE in longissimus dorsi muscle was significantly higher in males than in females. Association analysis revealed a sex-specific effect of this locus on body size traits. The A allele and AA genotype were significantly associated with increased body weight and heart girth in females, whereas no significant effect was detected in males. Therefore, the identified APOE gene mutation site can serve as a candidate molecular marker for the early selection of growth traits in Guizhou white goats. Full article

Background/Objectives: Salinity stress limits agricultural production and threatens global food security. Faba bean (Vicia faba L.) is an important legume crop, and identifying salt-stress-responsive genes may support an improvement in salt response. This study aimed to identify intronless genes in faba bean, screen candidate genes associated with salt-stress responses, and develop a KASP marker for salt-response evaluation. Methods: Intronless genes were identified from the faba bean reference genome. Transcriptome analysis was conducted in roots and leaves of two cultivars, Sucan 4 and Yundou 1183, under 150 mM NaCl treatment and control conditions. Candidate genes were examined by expression analysis, functional annotation, PPI prediction, and a luciferase complementation assay. A KASP marker was developed from an SNP within the VfERF1A locus and tested in 97 accessions. Results: A total of 7581 intronless genes were identified, accounting for 20.69% of annotated genes. Fifteen intronless genes were significantly differentially expressed in both roots and leaves of the two cultivars under salt treatment. Functional annotation suggested that VfERF1A and VfHSP17.8 may be involved in salt-stress responses. PPI prediction and the LUC assay provided preliminary support for a possible association of VfERF1A with VfEIN2. The VfERF1A-based KASP marker showed clear genotype clustering, and the two homozygous classes differed significantly in QYmax, relative shoot fresh weight, and relative plant height under salt treatment (p < 0.05). The preliminary predictive accuracy for QYmax was 86.36%. Conclusions: These results provide a genome-wide resource of intronless genes in faba bean, identify candidate genes associated with salt-stress responses, and describe a preliminary KASP marker associated with salt-response traits. Further validation in independent populations, under diverse environmental conditions, and with additional functional evidence is still required. Full article

Vertical transmission of plant pathogenic viruses is an important component of viral persistence, survival, and spread in agricultural production systems. This type of transmission is of considerable economic significance as it can cause major crop losses by serving as the initial focus of infection for future epidemics. Vertical transmission occurs when a virus is passed on to offspring either by direct invasion of the developing seed embryo from infected mother plants or through infected pollen grains after fertilization. We have recently demonstrated via high-throughput sequencing that mature seeds of the agriculturally important forage crop alfalfa (Medicago sativa L.) are associated with a broad range of viruses, some of which could potentially spread over long distances via seed. With the exception of the alfalfa mosaic virus, little is currently known about viral transmission through alfalfa pollen and its subsequent impact on the disease epidemiology of the crop. The objective of this study was to screen pollen from diverse alfalfa genotypes for pathogenic viruses and assess their risk of transmission. The pollen was collected from alfalfa genotypes selected for fungal disease resistance and agronomic performance in the USDA ARS pre-breeding program in Prosser, WA. Full article

Background: Although HPV vaccination is highly effective in the primary prevention of cervical cancer, its potential role in women already diagnosed with HPV-associated cervical dysplasia remains uncertain. This study aimed to evaluate the association between post-diagnosis HPV vaccination and short-term clinical outcomes in HPV-positive women with cervical dysplasia. Methods: Women aged ≥18 years with abnormal cervical screening results suggestive of squamous intraepithelial lesions and high-risk HPV positivity were retrospectively evaluated. High-grade disease was defined as histologically confirmed CIN2/3. HPV vaccination (9-valent) was recommended to all eligible patients at the time of diagnosis. Vaccination status was primarily analyzed as vaccinated (≥1 dose) versus unvaccinated; additionally, dose-stratified analyses (0, 1–2, and 3 doses) were performed to explore potential dose–response relationships. Results: A total of 392 women were included (173 unvaccinated and 219 vaccinated). At 12 months, regression occurred in 51.1% of vaccinated patients compared with 41.0% of unvaccinated women (OR 1.50, 95% CI 1.02–2.20, p = 0.04). A dose–response pattern was observed, with regression rates of 41.0% in unvaccinated patients, 46.1% in partially vaccinated patients, and 54.6% in fully vaccinated patients (p for trend = 0.012). In the HSIL subgroup, regression occurred in 49.0% of vaccinated women versus 33.8% of unvaccinated patients (OR 1.88, 95% CI 1.01–3.52, p = 0.047). When stratified by treatment modality, vaccination was significantly associated with higher regression in the non-LEEP cohort (OR 1.67, p = 0.04) but not in the LEEP cohort (p = 0.22). In multivariable analysis adjusting for age, smoking, HPV genotype, baseline histopathologic grade (CIN1 vs. CIN2/3), and treatment modality, HPV vaccination remained independently associated with regression (aOR 1.55, 95% CI 1.05–2.30, p = 0.028). Conclusions: Post-diagnosis HPV vaccination was associated with a higher probability of cervical dysplasia regression at 12 months, particularly among women with baseline HSIL. These findings suggest that HPV vaccination may provide a beneficial adjunct effect in the clinical management of HPV-associated cervical dysplasia. Prospective studies are required to confirm these observations and clarify the mechanisms underlying this association. Full article

Background/Objectives: The informative value of integrating high-risk human papillomavirus (HR-HPV) genotyping with cytology and p16/Ki67 dual-stain biomarker results, using limited and two types of extended genotyping assays, has not yet been evaluated. Methods: A total of 32,724 screening test results between 2015 and 2024 were included. Limited HPV genotyping was performed using the Abbott RealTime High Risk HPV assay. Extended genotyping was performed using two assays: the Alinity m HR HPV and BD Onclarity HPV Assay. Trends in age-specific, cytology-specific, and p16/Ki67-specific HR-HPV prevalence and distribution were observed, and differences between limited and extended genotyping were examined. Results: The overall HR-HPV positivity rate was 15.0%. HR-HPV prevalence was 13.9% in the limited genotyping group, 17.8% in in the Onclarity group 1, and 17.2% in the Alinity group 2, with a statistically significant difference in the proportions of positive/negative cases (p < 0.0001). No statistically significant difference was observed between extended genotyping groups (p = 0.706). In the Onclarity group: the highest p16/Ki67 positivity was observed for HPV 33/58 (100.0%) and HPV 31 (58.8%), while the lowest was for HPV 45 (18.2%), HPV 18 (25.0%) and HPV 59/56/66 (28.9%). In the Alinity group: the highest p16/Ki67 positivity was observed for HPV 16 (66.7%) and HPV 31/33/52/58 (58.8%). Conclusions: Based on ten years of HPV-based cervical cancer screening data, this study demonstrates that genotype-specific HR-HPV information obtained through extended genotyping provides clinically relevant risk stratification when interpreted together with cytology and p16/Ki67 dual-stain results. These findings support an integrated screening approach combining molecular HPV testing, cytology, and immunocytochemical biomarkers to improve risk-based triage in cervical cancer screening. Full article